Dear gmx-users, I wish to order the components of my system with respect to the polypeptide using trjorder.
I want to select my first group as the protein and the second group to be ordered is non-protein (i.e all other components in the system except polypeptide) the command I am using is: trjorder -f shape.gro -s shape.tpr -da 0 -o ordered.gro The problem is -na "int" is required, but the rest of my system contains TIP4P water, methanol, Li ions so the na is different for all non-protein components. Is there a way to override option -na and still get non-protein part of the system ordered with respect to the polypeptide (protein) Thanks, SN
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